vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
vector<string> Treenames;
- map<string, string> names;
+ //map<string, string> names;
vector<string> binLabelsInFile;
vector<string> currentBinLabels;
string saveNextLabel, argv, sharedHeaderMode;
int appendFiles(string, string);
int renameFile(string, string); //oldname, newname
string getFullPathName(string);
+ string findProgramPath(string programName);
string hasPath(string);
string getExtension(string);
string getPathName(string);
string getline(istringstream&);
void gobble(istream&);
void gobble(istringstream&);
- map<string, int> readNames(string);
+ vector<string> splitWhiteSpace(string& rest, char[], int);
+ vector<string> splitWhiteSpace(string);
+ set<string> readAccnos(string);
+ int readAccnos(string, vector<string>&);
+ map<string, int> readNames(string);
+ int readTax(string, map<string, string>&);
+ int readNames(string, map<string, string>&, map<string, int>&);
int readNames(string, map<string, string>&);
+ int readNames(string, map<string, string>&, bool);
int readNames(string, map<string, vector<string> >&);
int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
int mothurRemove(string);
void splitAtDash(string&, set<string>&);
void splitAtDash(string&, vector<string>&);
void splitAtChar(string&, vector<string>&, char);
+ void splitAtChar(string&, string&, char);
int removeConfidences(string&);
+ string makeList(vector<string>&);
//math operation
int factorial(int num);
int getRandomIndex(int); //highest
int control_pressed;
- bool executing, runParse, jumble, gui, mothurCalling;
+ bool executing, runParse, jumble, gui, mothurCalling, debug;
- //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
+ //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes.
string getPhylipFile() { return phylipfile; }
string getColumnFile() { return columnfile; }
string getListFile() { return listfile; }
string getAccnosFile() { return accnosfile; }
string getTaxonomyFile() { return taxonomyfile; }
string getFlowFile() { return flowfile; }
+ string getBiomFile() { return biomfile; }
string getProcessors() { return processors; }
void setListFile(string f) { listfile = getFullPathName(f); }
void setAccnosFile(string f) { accnosfile = getFullPathName(f); }
void setTaxonomyFile(string f) { taxonomyfile = getFullPathName(f); }
void setFlowFile(string f) { flowfile = getFullPathName(f); }
- void setProcessors(string p) { processors = p; }
+ void setBiomFile(string f) { biomfile = getFullPathName(f); }
+ void setProcessors(string p) { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n"); }
void printCurrentFiles();
bool hasCurrentFiles();
void clearCurrentFiles();
+ set<string> getCurrentTypes();
private:
static MothurOut* _uniqueInstance;
taxonomyfile = "";
processors = "1";
flowfile = "";
+ biomfile = "";
gui = false;
printedHeaders = false;
commandInputsConvertError = false;
mothurCalling = false;
+ debug = false;
sharedHeaderMode = "";
}
~MothurOut();
string defaultPath, outputDir;
string releaseDate, version;
- string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
+ string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
vector<string> Groups;